Command not found

[dfournier013]

Hello,

Thank you for developing this code, I know it will be invaluable once I can get it working. I'm working on a Mac and trying to execute the "menextract2pdf_overwrite.sh" command after navigating to the the unzipped file, but an error message saying "command not found" pops up.

I've tried putting the folder in the same mendeley desktop folder in application support and in other folders not containing anything relevant to mendeley (i.e. download folders) with no luck.

Any help would be greatly appreciated, I'm sure this due to my inexperience working within terminal and I've found very little help on other sites. I was following instructions from (https://www.zotero.org/support/kb/mendeley_import#preserving_mendeley_annotations_and_highlights)

Thank you!

[spcanelon]

Not a solution, but perhaps a little closer? 🤷‍♀️
I at least got the script to run and find the PDFs, etc. but what I got was mostly warnings associated with the PDFs getting processed. These are the warnings/errors I came across:

• UserWarning: Unable to resolve [IndirectObject: IndirectObject(77, 0)], returning NullObject instead [pdf.py:595]
• zlib.error: Error -3 while decompressing data: incorrect header check

I'm also not super experienced with terminal and ran into this issue. I realized I didn't have the package dependencies installed that are pointed out in the README.md:

• PyPDF2
• sqlite3

Someone asked about installing PyPDF2 online and an answer suggested installing Python 3.

With that to go on, here's what I did:

1. Install Python 3. Resource: https://theptrk.com/2020/05/02/how-to-install-python-3-on-mac-using-homebrew/

brew install python

2. Install PyPDF2. Resource: https://pypi.org/project/PyPDF2/

pip3 install PyPDF2

The installation was fine but the script didn't end up finding PyPDF2, so I tried this solution from @strophios instead which was to download PyPDF2 directly from GitHub and copy the PyPDF2 folder into the /src folder within Menextract2pdf-master.

3. Install sqlite3. Resource: https://formulae.brew.sh/formula/sqlite

brew install sqlite

4. Run menextract2pdf command as suggested on the Zotero site. Note the ./ at the start (suggested by an answer on Stack Overflow and the two underscores between "menextract2pdf" and "overwrite.sh"

./menextract2pdf__overwrite.sh "/Users/"Your Name"/Library/Application Support/Mendeley Desktop" "/Users/"Your Name"/Library/Application Support/Mendeley Desktop/Downloaded/"

[strophios]

Just want to add to @spcanelon's last point (because I also ran into the "command not found" error and didn't know why): I found another stackoverflow answer with a bit more info on why you need the ./. Namely, because only scripts in one of the directories in your $PATH can be executed directly (i.e. with only the file name).

[spcanelon]

Zotero Beta now supports the import of PDF highlights and annotations!

The Zotero Mendeley import guide was last updated 3/11/2021: https://www.zotero.org/support/kb/mendeley_import

To import PDF highlight and note annotations, you currently must import using the Zotero Beta, which adds support for annotations.